scholarly journals A novel allele of the P-starvation tolerance gene OsPSTOL1 from African rice (Oryza glaberrima Steud) and its distribution in the genus Oryza

2014 ◽  
Vol 127 (6) ◽  
pp. 1387-1398 ◽  
Author(s):  
Juan Pariasca-Tanaka ◽  
Joong Hyoun Chin ◽  
Khady Nani Dramé ◽  
Cheryl Dalid ◽  
Sigrid Heuer ◽  
...  
Keyword(s):  
Oryza Glaberrima ◽  
African Rice ◽  
Starvation Tolerance ◽  
Genus Oryza ◽  
Tolerance Gene ◽  
Novel Allele

scholarly journals The African Rice Oryza glaberrima Steud: Knowledge Distribution and Prospects

2012 ◽  
Vol 4 (3) ◽  
Author(s):  
Yves Agnoun ◽  
Samadori S. H. Biaou ◽  
M. Sié ◽  
R. S. Vodouhè ◽  
A. Ahanchédé
Keyword(s):  
Oryza Glaberrima ◽  
African Rice

scholarly journals High-throughput phenotyping reveals a link between transpiration efficiency and transpiration restriction under high evaporative demand and new loci controlling water use-related traits in African rice, Oryza glaberrima Steud.

2021 ◽  
Author(s):  
Pablo Affortit ◽  
Branly Effa Effa ◽  
Mame Sokhatil Ndoye ◽  
Daniel Moukouanga ◽  
Nathalie Luchaire ◽  
...  
Keyword(s):  
Water Use Efficiency ◽  
Water Use ◽  
Association Studies ◽  
Crop Improvement ◽  
Oryza Glaberrima ◽  
Genome Wide Association Studies ◽  
Transpiration Efficiency ◽  
Evaporative Demand ◽  
African Rice ◽  
Use Efficiency

Because water availability is the most important environmental factor limiting crop production, improving water use efficiency, the amount of carbon fixed per water used, is a major target for crop improvement. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand, remain unknown. These traits were measured in a panel of 147 African rice Oryza glaberrima genotypes, known as potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly differentiated genotypes confirmed these associations and suggested that the root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency and its residuals, that links to genes involved in water transport and cell wall patterning. Our data suggest that root shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.

scholarly journals The complex geography of domestication of the African rice Oryza glaberrima

PLoS Genetics ◽  
2019 ◽  
Vol 15 (3) ◽  
pp. e1007414 ◽  
Author(s):  
Jae Young Choi ◽  
Maricris Zaidem ◽  
Rafal Gutaker ◽  
Katherine Dorph ◽  
Rakesh Kumar Singh ◽  
...  
Keyword(s):  
Oryza Glaberrima ◽  
African Rice

scholarly journals Sequence Variants Linked to Key Traits in Interspecific Crosses between African and Asian Rice

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1653
Author(s):  
Hayba Badro ◽  
Marie-Noelle Ndjiondjop ◽  
Agnelo Furtado ◽  
Robert Henry
Keyword(s):  
Association Analysis ◽  
Agronomic Traits ◽  
Heading Date ◽  
Sucrose Metabolism ◽  
Interspecific Crosses ◽  
Oryza Glaberrima ◽  
Gene Pools ◽  
Synonymous Snps ◽  
African Rice ◽  
Asian Rice

Asian and African rice gene pools vary in many traits that are important in rice breeding. The genetic basis of these differences was evaluated by analysis of important agronomic traits in crosses between African and Asian rice. Trait-associated variants (TAVs) influencing three quantitative agronomic traits, heading date (Hd), tiller number at maturity (T), and 1000 grain weight (TGW), were identified by association analysis of crosses between Asian and African rice. Populations were developed by crossing WAB56-104 (Oryza sativa) and CG14 (Oryza glaberrima). DNA from plants with extremely high or low values for these phenotypes was bulked and sequenced. The reference genome of O. sativa cv Nipponbare was used in general association analysis and candidate gene analysis. A total of 5152 non-synonymous single nucleotide polymorphisms (SNPs) across 3564 genes distinguished the low and the high bulks for Hd, T, and TGW traits; 611 non-synonymous SNPs across 447 genes were found in KEGG pathways. Six non-synonymous SNPs were found in the sequences of LOC107275952, LOC4334529, LOC4326177, LOC107275432, LOC4335790, and LOC107275425 genes associated with Hd, T, and TGW traits. These genes were involved in: abscisic-acid biosynthesis, carotenoid biosynthesis, starch and sucrose metabolism, and cytokinin biosynthesis. Analysis of 24 candidate genes associated with Hd, T, and TGW traits showed seven non-synonymous variations in the sequence of Hd3a and Ehd2 from the Hd genes (not in a KEGG pathway), D10 and D53 from the T genes (strigolactones biosynthetic pathway), and Gn1a and GIF1 from the TGW genes (cytokinin biosynthetic and starch and sucrose metabolism pathways). This study identified significant differences in allele frequencies supported by high sequence depth in analysis of bulks displaying high and low values for these key traits. These trait-associated variants are likely to be useful in rice improvement.

scholarly journals Comparison of two African rice species through a new pan-genomic approach on massive data

2018 ◽  
Author(s):  
Cécile Monat ◽  
Christine Tranchant-Dubreuil ◽  
Stefan Engelen ◽  
Karine Labadie ◽  
Emmanuel Paradis ◽  
...  
Keyword(s):  
Core Genome ◽  
Oryza Glaberrima ◽  
Large Core ◽  
African Rice ◽  
Asian Rice ◽  
External Reference ◽  
Genomic Approach ◽  
Cultivated Species ◽  
Group Species ◽  
High Depth

AbstractPangenome theory implies that individuals from a given group/species share only a given part of their genome (core-genome), the remaining part being the dispensable one. Domestication process implies a small number of founder individuals, and thus a large core-genome compared to dispensable at the first steps of domestication. We sequenced at high depth 120 cultivated African rice Oryza glaberrima and of 74 wild relatives O. barthii, and mapped them on the external reference from Asian rice O. sativa. We then use a novel DepthOfCoverage approach to identif missing genes. After comparing the two species, we shown that the cultivated species has a smaller core-genome than the wild one, as well as an expected smaller dispensable one. This unexpected output however replaces in perspective the inadequacy of cultivated crops to wilderness.

scholarly journals Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud)

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 376
Author(s):  
Peterson W. Wambugu ◽  
Marie-Noelle Ndjiondjop ◽  
Robert Henry
Keyword(s):  
Oryza Glaberrima ◽  
Trait Variation ◽  
African Rice ◽  
Sequencing Technologies ◽  
Climate Resilience ◽  
Sequencing Studies ◽  
Important Trait ◽  
Genetics And Genomics ◽  
Rice Improvement ◽  
Rice Genetic

African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.

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